The new SW BOM allows you to link a drawing view's balloons to an existing BOM. This means that you can have a drawing view of a particular configuration of the model, and then a view of another config (such as without the covers, belt guards, etc.) and still have the balloons match. The Excel based BOM had difficulties with that scenario.
Here is what the SW help file says about this under the Drawing View Properties category.
"Bill of Materials (BOM). Keep linked to BOM. Overrides the automatic linking of a BOM to a drawing view. As long as the BOM exists and Keep linked to BOM is selected, the SolidWorks software uses the selected BOM to assign balloon numbers. If you attach a balloon to a component that is not in the BOM configuration, the balloon appears with an asterisk (*)."
This means that if your "secondary" view assy config has a part in it that is not the same config as the part in the "main" view, you will get an asterisk in your balloon. You then have 2 choices - either change the config of the piece part to match the "main" config piece part config, or don't balloon it in that view.